


Embracing Fatherhood

by greekowl87



Category: The X-Files
Genre: AU, Baby William, F/M, Fluff, MSR, Maybe - Freeform, Mild Angst, Season 9 AU, Willian Van De Kamp, should this continue?
Language: English
Status: In-Progress
Published: 2018-05-21
Updated: 2018-05-27
Packaged: 2019-05-09 18:54:22
Rating: General Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 2
Words: 3,550
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/14721698
Author URL: https://archiveofourown.org/users/greekowl87/pseuds/greekowl87
Summary: AU. Should this continue? Mulder refuses to leave his new family when Kersh comes and warns about a threat against his life.





	1. Chapter 1

Scully slept beside Mulder in their bed as he sat up against the headboard, unable to sleep. Kersh had come two days earlier warning of an attempt that would be made on Mulder’s life, just after Scully had delivered their son into the world, he was faced with another precarious decision. He looked down beside him and raked his fingers through Scully’s hair and she murmured her name in his sleep. Mulder bent down and kissed her hair before getting out of bed and quietly tiptoeing over to the bassinet by Scully’s side of the bed. He was surprised to see his son wide awake, his alert baby blue eyes watching the mobile that he had installed weeks before.

“Whatcha doing, little man,” he whispered, lifting up his son securely in the crook of his arm. Baby William made a gurgling happy sound and Mulder kissed his brow gently. “Let’s not wake mommy, huh?”

With one last glance, he shut the door slightly and carried William out with him into the living room where he turned on the television. Mulder looked down at his son and whispered, “You know, when I came back and saw Scully pregnant, I didn’t know what to do.”

William wasn’t a big baby but somehow, he fit perfectly in Mulder’s arm. “That’s not to say I didn’t want you, bud. I just…” he paused, in thought. He felt weird talking so deeply with a baby but somehow, the fact it was his son made all the difference. “I should have seen the signs, Will, in the beginning before I was abducted. Your mother’s morning sickness, the cravings…” His voice faded in thought as Mulder flipped to a black and white movie.

“Okay, here’s a classic, bud. Plan 9 From Outer Space.”

Mulder heard William whimper and frowned. “What is? Diaper?” He sniffed William’s bottom and shook his head. “Hungry then. You know, you eat like your mother.”

He got up, still holding William and warmed up a bottle while he hummed absently, marveling at his son. As the microwave dinged, he began to the feed the baby. Walking back to the living room, he could hear William suckling greedily.

“I know it’s not the real thing, and I don’t blame you if you’re hungry, especially when mommy is feeding you,” he chuckled.

Never in a million years would he had imagined this or the happiness that would ensue knowing he had a family…that he was now a father and partner, a life partner he clarified, with expectations and responsibilities. They settled back on the couch with his son, Mulder gazed at the television in thought listening to his son suckle hungrily at the bottle. “You know, Will, my dad was never around.” He thought of the smoking man and the Bill Mulder. “Always busy. I thought I was doomed from the start. Cursed genes, Will. I hated myself. I hated everything and then mommy walked in wearing that horrible plaid jacket and she was so…”

“What?” a warm voice piped from the bedroom.

Mulder looked up and saw Scully stroll over and melt next to Mulder. “I was telling Will about when we met.”

“Oh, continue. Pretend I’m not here.”

“Mommy scared daddy,” Mulder whispered, wrapping his arm around Scully. “She was short but smart. Tough but scary.”

“I was not.”

They both watched William’s eyes dance between them. “I was scared, bud. I don’t know about mommy.” He kissed her hair. “But when daddy came back from being gone, he was scared.” Scully quieted, listening to him to speak about his abduction. “I was scared mommy didn’t want me. She was pregnant with you. I know you were mine…ours. But I was so scared. I had already missed so much. Why would she want me back? Spooky Mulder comes back from the dead.” Scully squeezed his arm. “But lucky for us, bud, mommy is the most amazing person in the world.”

“I always wanted you,” she murmured.

“I know that now. I was thinking, Scully. I don’t want to go. I don’t want to leave.”

“I wasn’t asking you to. Not again. I don’t think I could handle it.”

“I know we talked about it but I don’t want to leave again. I am not going to run.”

Tears came to Scully’s eyes and she kissed him soundly. “Whatever the future holds?”

“We handled it together, as a family,” he vowed.

William fussed and Mulder frowned. “I think he wants the real thing.”

She chuckled sleepily and took their son from him. “I’m glad we are together,” she murmured into his bicep. “For good. We never worked well when we were separated.”

“No. We didn’t.” He held them both. “It’s going being difficult.”

“We’ll figure it out. Mulder,” she whispered, looking up at him. “You have no idea how happy I am.”

He kissed her brow and looked at their son. “I have an idea. Kersh is lying. I’m not leaving, Scully.”

“I’m glad, Mulder,” she whispered. “Nothing we can’t face together.”


	2. Nothing Important Happened Today Pt I

**Notes for the Chapter:**

> I’m still trying to decide how to go about doing this project and trying to stick with it. It’s been so long since I watched season 9 and it’s been cringe-worthy especially knowing how the cannon goes. But I am going to have to rewatch the season. I also don’t know the direction this is going to go (except having Mulder and Scully together as a family–as it should have been). So the first two episodes will be tackled in two chapters but consider this a blurb for the time being while I try to get my thoughts together about it.
> 
> The original dialogue to the episode doesn't belong to me. Just borrowing.

Scully eyed the bags as she absently rocked William and listened to Mulder in the shower. In a collection of about six suitcases of various sizes, Mulder had packed away his life in six suitcases and moved effectively out of his Alexandria apartment. Her thoughts in the back of her mind danced with a reality without Mulder in their lives, hers and their sons, but she silently thanked God that he had finally come to his senses and decided to stay with them. As she walked around, hushing William, Mulder emerged from the shower, his hair sticking up in all various ways.

He smiled at Scully and noticed the new warm smile she had and that motherly glow that seemed to illuminate her entire being. He wrapped a towel around his waist and nodded to her. “Being a mother becomes you.”

“Being a father becomes you,” she responded.

They shared a kiss and Mulder cooed at the baby in her arms. “Are you behaving for mommy?”

“I just had my bottle, daddy,” Scully whispered, jousting Will playfully. Mulder caressed his son affectionately and kissed Scully. “We were just about to take a nap. Daddy should join me because mommy said you weren’t sleeping very well.” Their eyes met. “You need to sleep, Mulder. I know you couldn’t last night.”

“I’m just worried,” he whispered softly. “Kersh’s threat still is in the back of my mind. I still wonder…”

“No,” she corrected swiftly. “Your place is here with your family now.” Scully’s quickly shut down any lingering thoughts he may have had about staying with his new family and putting them in danger. “Mulder, we both discussed this. We stand a better chance together. Both of our abductions should at least demonstrate that.”

He nodded in affirmation. “I’m going to lay down for a bit.”

“Good,” Scully admonished. She passed Mulder their sleepy newborn son and he began to bounce William soothingly. She kissed the baby’s head and turned to her partner. “I’ll leave the phone off the hook so you can get some sleep.”

“It’s nice we can still spend some time together with your maternity leave,” he added in afterthought, “however, why are you dressed like you are about to go to work?”

“We have a late lunch with my mother, remember? You two get some rest. I’ll find something to keep me busy.”

“Scully,” he called, pausing with William at the door.

“Hmm?”

“Love you.” The warmth of his words spread through her and she gave him a gentle smile in response.

. . . .

Scully watched them from the doorframe of her, no, she corrected mentally, their bedroom as Mulder slept shirtless on his side and William slept just as soundlessly in the bassinet by her side of the bed. All those months ago, when she first began to show in the stages of her pregnancy, she tried to get used to the idea of being a single mother, raising her unborn child alone, and trying to explain who the dead father was. Sure, her family would help her raise the child, but it would not have been the same. She remembered having to lower his body into the ground and with that coffin, she went to. When he came back, after the first difficulties of dealing with everything for both of them, but when William was born, everything changed yet again. He was her other half and William their soul. When they both made the decision to stay as a family, they also decided that Scully was going to remain with the FBI and teach at Quantico and Mulder, after a lot of thought and talking to one of the agents who he used to work within VCU and now ran the criminal psychology department at the FBI academy, Mulder would return, not as an agent, but a tenured lecturer (all those years of experience and Oxford degrees were hard to overlook).

Her thoughts were brought back to the present, which she was glad to do, but there were still things on her mind. With the birth of their son, they promised each other that this was the end for them and the x-files. The dangerous path that had brought them together was at an end and a new road lay before them. They were done with the x-files and chasing monsters in the dark. Now they had a son to think of. Scully gave a small smile and closed the bedroom door for her men and went to her desk to lift the phone off the receiver to keep from having any disturbances.

As she eyed the suitcases still sitting in her living room and still tried to wrap her mind around everything was happening. Mulder was here. They were together, as they always should have been. Mulder was embracing fatherhood just like she would fantasize about during the months she was still searching for him. And now he was here. They had a family and a son to raise. They had finally gotten their happy ending and like hell, she was going to give that up.

. . . .

Scully sat at her kitchen table, quietly reviewing a very much delayed and overdue journal article for some sense of normalcy but she found herself smiling at the thought of this being the new normal. She suddenly heard a ringing of her cell phone in her briefcase. She rushed hurriedly and turned it off, ignoring who was calling so that she would not wake Mulder or their son. Suddenly there was a rapid knocking at her door. Sighing, Scully wondered who could be there, praying it wasn't her mother.

She eyed the peephole and saw Agent John Doggett standing on the other side, his face wrought with worry. She opened the door slightly, keeping the back of her foot propped against the door as if protecting her and her new family from her past. "What? What's the matter?"

Doggett's eyes widened as if she had grown a third head. "What's the matter? I've been trying to call you."

"Yeah, the phone's off the hook because of the baby. He's sleeping."

"I got panicked that you're not going to be here, that you left, too."

She was quiet as she thought raced at what he was talking about. Mulder has packed hurriedly and rushed over to her apartment shortly after William's birth with the Gunman's help and the Alexandria apartment had been quickly cleared out with their help. Scully opened the door more. "Come in."

Doggett stormed past her, his head moving to and fro as if looking for something. "I've been looking for Mulder. I went to his apartment."

"I know."

"Where'd he go?" Doggett pressed.

Scully remained silently, battling internally as if admitting Mulder was just beyond her bedroom door would break any fantasy that she had been building up.

"Dana... where'd he go?" Doggett asked emphatically.

Scully looked at Doggett and sighed. "He's sleeping. Along with the baby."

"Why is he still here? Kersh told him to run."

"I lost him once," Scully said determinedly. "I'm not losing him again. We face this as we always have. Together."

Doggett looked away and sighed. "What about the baby, Dana?"

"We are doing this for our son, John." She took a deep breath. "Now, if you don't mind, would you please leave?"

Doggett did as he was told, like a man used to following orders. The door shut with finality and Scully jumped when she heard Mulder's monotone sleepy voice come from the bedroom. "Was that the pizza man?"

Scully shook her head, feeling suddenly overwhelmed. Doggett's presence served as a reminder that her past was still there and that it would always be there. She was suddenly enveloped by Mulder's embrace as she snaked her arms around his neck. "I won't let the darkness back into our lives, Mulder. Not again. We are finally free and I'm not going back there."

"What about the threats, Scully?"

She shrugged. "That's why we agreed for you to teach at Quantico. I'm not letting you at my sight."

He buried his nose in her hair. "You know, we could enact some sexual fantasies in *your* office on your *desk*."

She laughed and felt her fears ebb and simply let him hold her. "Is William okay?"

"Sleeping just like his mother. Why don't you sit down? I'll make us something to eat, okay?"

In a rare display of affection, which Mulder sensed would become more commonplace, she kissed him soundly and nodded in agreement.

. . . .

As the day continued, Scully's fears and the darkness abated as she just learned to enjoy just simply being in the moment. Shortly after their early lunch, William woke up, crying, and Mulder got him from the bedroom and passed him off to Scully for his lunchtime. The new parents enjoyed watching their newborn as he cooed and gurgled. After lunch, Scully decided to try and get their son back down for another nap. Mulder pressed a kiss to forehead and whispered, "I'm going to go work on his crib while you put King William down for a nap."

"King William?" Scully chuckled.

"The kid gets the best view in the house and he has both of us waiting on him hand and foot. He's the king now and we are his royal servants. Now if you excuse me, this serf has a crib to assemble."

"Call me..."

"I got it, Scully. Put the king down for his afternoon nap, okay?"

She gave him a dazzling smile and he shook his head, his laughter echoing into the baby's new room. Scully looked down at sleepy William and whispered, "He's such a spooky nerd, you know that, William. You know, I wasn't thinking ahead when I gave your name. Your Uncle Bill will think I named you after him but you are named after your grandfathers, both your grandfathers really but that's a big name to grow into. What about a nickname?" His baby-faced scrunched up in distaste. "Oh, it's not all that bad. What about Liam?" He made a noise suggesting distaste. "Okay, Iam?" She pronounced it like 'Ian' but drew out the' sound.

Mulder appeared briefly and asked. "Just call him Ian at that? I am sounds weird, Scully."

"Ian?"

William cooed and Mulder shrugged as if saying, 'I told you so.'

"Ian," Scully repeated, "just because your father is lazy."

"Don't listen to her, Will. Laziness is a sign of genius."

"Serf, go do your work. Our king demands it."

Mulder grinned and shut the door behind him as he disappeared into the construction of William's ever-evolving bedroom. Scully patted the baby's back and whispered, "I hope you are just as lucky, William. But your father and me...we've been through so much. We really are lucky, you and me." She bounced William up and down absently. "We are going to stay together no matter what. Maybe one day, we'll have a proper wedding. How would you like that, Will?"

He hiccupped sleepily.

"Or Ian?"

He grunted.

"Will then. Daddy doesn't know what he is talking about."

Suddenly the door opened and Scully shifted William onto her shoulder to look into the peephole and sighed when she saw John. She opened the door and he sighed, looking at her. " I'm really sorry. I... Dana, I need your help."

Scully stood like a wall in the doorway. "I told you no, John."

"Dana, I wouldn't be here if it wasn't important."

Scully sighed and let him into the apartment. "Give me a minute while I put William to sleep."

Doggett watched her retreating back and strained his ears to hear something coming from the bedroom. "Scully? That better not be the pizza boy again!"

Mulder emerged and regarded Doggett quietly. "Agent Doggett, a surprise to see you here."

"Mulder," John nodded stiffly, shifting his weight uneasily.

Mulder watched him wearily. "What are you doing here?"

"I could ask you the same. It just doesn't make any sense. You should be gone if you want to keep Dana safe and your son."

"It makes sense in its own way. That's all I can tell you." Scully emerged from the bedroom and glanced at Mulder, silently assessing the situation.

"Then tell me why you can't trust me. Everything I did to try and protect you when you thought your baby was in danger. What changed? Why is it suddenly I'm now the enemy?" Doggett asked angrily. "I came to you asking for help, asking for Mulder's help. I can't do this alone."

Scully crossed the living room and stood at Mulder's side. Without hesitation, his hand went to the small of her back. She glanced at her partner and rested her hand on Mulder's chest. "I told you why. Let it go, John. Drop it. Please."

Doggett's eyes bugged out, pleading with them. "These people tried to kill me. They tried to kill AD Skinner. They wanted to kill Mulder, too. They're still out there, Dana."

"It comes with the territory, John. I'm not doing it anymore. We're not doing it anymore, me or Mulder. Exactly right, and they are unstoppable, and they are inside the FBI. We won't risk our family."

Mulder stood silently by Scully's side, trusting her to do the talking. John's eyes darted between them. "You know something you're not telling me. Mulder knows something." His gaze lingered on him. "How long can you hide it from me? Knowle Rohrer, this old military buddy of mine. He told me your pregnancy was a result of a Government cloning experiment to try to create what he called a Super Soldier."

"I don't want to hear this. Look, there is nothing to any of this." Scully broke away from Mulder, wrapping her arms around herself. "Stop it."

"Knowle Rohrer, my buddy, was one of the men that tried to kill us in the FBI garage."

Mulder hissed and grabbed Doggett by the shoulder. "Stop it. Now."

"My baby... my son... is fine," Scully spoke slowly, punctuating each word. Mulder reached out, catching her hand to pull her back to his chest. "Our son is fine."

Doggett swallowed the lump in his throat. "I hope to God that's true. I just don't want to pretend."

Mulder kissed her forehead wordlessly and Scully took a deep breath. "I'm going to ask you to leave."

Mulder watched Agent Doggett's jaw hanging open loosely before Scully ordered without emotion, "I'm going to ask you to leave and not come back here."

Mulder's arms coiled around Scully as she closed her eyes. John said nothing but left without another word, closing the door behind him. Scully looked up into Mulder's warm hazel eyes with tears and he saw how afraid she was. Wordlessly, he just held her tightly and rocked her to ease her fears.

. . . .

Mulder had urged Scully to take another nap after their confrontation with Doggett. Seeing his partner distressed killed him inside. She whispered soothingly to William as he struggled back to sleep and settled down on her side of the bed. She could hear Mulder out int he living room and she let the comforting sounds lull her with Mulder watching tv. Suddenly, William began to cry, and then the mobile began to spin. She got up thinking it was the wind from an open window but as she stood over the crib, watching William cry and the mobile spin unaided. Her worst fears were sinking into he heart as she reached out to stop the spinning mobile and pull back her hand as it continued to spin over William's crying. All of Doggett's warnings came flooding back and she heaved a dry sob in fear.

"Mulder. Mulder!"

Her partner was quick to break into their bedroom and saw Scully's despondent look. Mulder's heart broke seeing the fear in her eyes. Wordless communication flowed between them as he took her hand pulled her to his chest an embrace as they watched the mobile spin under William's power.

"We need to call Doggett," Mulder whispered.

She nodded, hugging him tightly. "Together, Mulder?"

"Always, Scully. Always." He looked at their son, a deep, powerful emotion welling in his chest. He vowed, “I’ll take care of both of you. I’m not going anywhere.”


End file.
